Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999999328 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM081556)
  • known disease mutation: rs18371 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:233391374T>CN/A show variant in all transcripts   IGV
HGNC symbol CHRND
Ensembl transcript ID ENST00000543200
Genbank transcript ID N/A
UniProt peptide Q07001
alteration type single base exchange
alteration region CDS
DNA changes c.188T>C
cDNA.244T>C
g.672T>C
AA changes L63P Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 63
frameshift no
known variant Reference ID: rs121909508
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs18371 (pathogenic for Congenital myasthenic syndrome 3B) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM081556)

known disease mutation at this position, please check HGMD for details (HGMD ID CM081556)
known disease mutation at this position, please check HGMD for details (HGMD ID CM081556)
regulatory features Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)4.1011
4.7431
(flanking)1.0091
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally decreased681wt: 0.9492 / mu: 0.9213 (marginal change - not scored)wt: ACTCTCCAACCTCATCTCCCTGGTGAGAGGCCCTCCGGTGC
mu: ACTCTCCAACCCCATCTCCCTGGTGAGAGGCCCTCCGGTGC		 ccct|GGTG
Acc increased669wt: 0.33 / mu: 0.41wt: CCTGGCCCTCACACTCTCCAACCTCATCTCCCTGGTGAGAG
mu: CCTGGCCCTCACACTCTCCAACCCCATCTCCCTGGTGAGAG		 ccaa|CCTC
Acc marginally increased679wt: 0.3647 / mu: 0.3686 (marginal change - not scored)wt: ACACTCTCCAACCTCATCTCCCTGGTGAGAGGCCCTCCGGT
mu: ACACTCTCCAACCCCATCTCCCTGGTGAGAGGCCCTCCGGT		 ctcc|CTGG
Acc marginally increased672wt: 0.2346 / mu: 0.2380 (marginal change - not scored)wt: GGCCCTCACACTCTCCAACCTCATCTCCCTGGTGAGAGGCC
mu: GGCCCTCACACTCTCCAACCCCATCTCCCTGGTGAGAGGCC		 acct|CATC
distance from splice site 11
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      63VDVALALTLSNLISLGWTDNRLKW
mutated  not conserved    63SNPISLGWTDNRLK
Ptroglodytes  all identical  ENSPTRG00000013040  63SNLISLKEVEETLTTNVWIEHGWTDNRLK
Mmulatta  all identical  ENSMMUG00000022147  63SNLISLKEVEETLTTNVWIEHGWTDNRLK
Fcatus  all identical  ENSFCAG00000005679  62SNLISKEVEETLTTNVWMEHGWTDPRLQ
Mmusculus  all identical  ENSMUSG00000026251  66LTLSNLISLKEVEETLTTNVWIDHAWVDSRLQ
Ggallus  all identical  ENSGALG00000007899  60VDVYLALTLSNLISLK
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000019342  63VDIYLALTLSNLISLKEVDETLLTNVWME
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000027884  63VNVSLALTLSNLISLKEA
protein features
start (aa)end (aa)featuredetails 
22245TOPO_DOMExtracellular (Potential).lost
9797CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
151151DISULFIDBy similarity.might get lost (downstream of altered splice site)
164164CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
165165DISULFIDBy similarity.might get lost (downstream of altered splice site)
246270TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
278299TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
312333TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
334471TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
390390MOD_RESPhosphotyrosine; by Tyr-kinases (By similarity).might get lost (downstream of altered splice site)
472490TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1509 / 1509
position (AA) of stopcodon in wt / mu AA sequence 503 / 503
position of stopcodon in wt / mu cDNA 1565 / 1565
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 57 / 57
chromosome 2
strand 1
last intron/exon boundary 1383
theoretical NMD boundary in CDS 1276
length of CDS 1509
coding sequence (CDS) position 188
cDNA position
(for ins/del: last normal base / first normal base)		 244
gDNA position
(for ins/del: last normal base / first normal base)		 672
chromosomal position
(for ins/del: last normal base / first normal base)		 233391374
original gDNA sequence snippet GGCCCTCACACTCTCCAACCTCATCTCCCTGGTGAGAGGCC
altered gDNA sequence snippet GGCCCTCACACTCTCCAACCCCATCTCCCTGGTGAGAGGCC
original cDNA sequence snippet GGCCCTCACACTCTCCAACCTCATCTCCCTGGGCTGGACAG
altered cDNA sequence snippet GGCCCTCACACTCTCCAACCCCATCTCCCTGGGCTGGACAG
wildtype AA sequence MEGPVLTLGL LAALAVCGSW GLNEEERLIR HLFQEKGYNK ELRPVAHKEE SVDVALALTL
SNLISLGWTD NRLKWNAEEF GNISVLRLPP DMVWLPEIVL ENNNDGSFQI SYSCNVLVYH
YGFVYWLPPA IFRSSCPISV TYFPFDWQNC SLKFSSLKYT AKEITLSLKQ DAKENRTYPV
EWIIIDPEGF TENGEWEIVH RPARVNVDPR APLDSPSRQD ITFYLIIRRK PLFYIINILV
PCVLISFMVN LVFYLPADSG EKTSVAISVL LAQSVFLLLI SKRLPATSMA IPLIGKFLLF
GMVLVTMVVV ICVIVLNIHF RTPSTHVLSE GVKKLFLETL PELLHMSRPA EDGPSPGALV
RRSSSLGYIS KAEEYFLLKS RSDLMFEKQS ERHGLARRLT TARRPPASSE QAQQELFNEL
KPAVDGANFI VNHMRDQNNY NEEKDSWNRV ARTVDRLCLF VVTPVMVVGT AWIFLQGVYN
QPPPQPFPGD PYSYNVQDKR FI*
mutated AA sequence MEGPVLTLGL LAALAVCGSW GLNEEERLIR HLFQEKGYNK ELRPVAHKEE SVDVALALTL
SNPISLGWTD NRLKWNAEEF GNISVLRLPP DMVWLPEIVL ENNNDGSFQI SYSCNVLVYH
YGFVYWLPPA IFRSSCPISV TYFPFDWQNC SLKFSSLKYT AKEITLSLKQ DAKENRTYPV
EWIIIDPEGF TENGEWEIVH RPARVNVDPR APLDSPSRQD ITFYLIIRRK PLFYIINILV
PCVLISFMVN LVFYLPADSG EKTSVAISVL LAQSVFLLLI SKRLPATSMA IPLIGKFLLF
GMVLVTMVVV ICVIVLNIHF RTPSTHVLSE GVKKLFLETL PELLHMSRPA EDGPSPGALV
RRSSSLGYIS KAEEYFLLKS RSDLMFEKQS ERHGLARRLT TARRPPASSE QAQQELFNEL
KPAVDGANFI VNHMRDQNNY NEEKDSWNRV ARTVDRLCLF VVTPVMVVGT AWIFLQGVYN
QPPPQPFPGD PYSYNVQDKR FI*
speed 1.32 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project